My 2.5 year old son is showing a stuffy nose, sore throat, general lethargy, loss of appetite and reduced defecation frequency. what could it be?

Viral infection: A viral infection or strep throat can present with those symptoms. If he is peeing well then he is probably not dehydrated...Decreased pooping makes me wonder about his hydration status especially with lethargy. You do not mention fever...Flu can also be a consideration and usually has fever with it. Make an appointment for him to be seen.

Not strep: Streptococcal throat infections do not cause a runny nose. If runny nose is present, one can generally rule out strep infection. When 2 yo get sick, they don't eat well & get pretty droopy from malaise & fever. If they don't eat or drink well they don't poop much. You describe a typical toddler viral cold. He should be checked if fever persists more than 3 days or he doesn't pep up.